---
title: " "
output: 
  flexdashboard::flex_dashboard:
    source_code: embed
    theme: united
    social: menu
    css: style2.css
    logo: logo.png
    
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(
	echo = FALSE,
	message = FALSE,
	warning = FALSE
)
library(flexdashboard)
library(prettydoc)
library(readxl)
library(tidyverse)
library(crosstalk)
library(plotly)
library(viridis)
library(gsheet)
library(leaflet.providers)
library(leaflet)
library(DT)
library(cowplot)
```



```{r load data, message=FALSE, warning=FALSE, include=FALSE}
Sys.setlocale("LC_ALL", "pt_BR.UTF-8")


mg_prod <- gsheet2tbl("https://docs.google.com/spreadsheets/d/13xAflAQ-x78Vkq0O0jUEkUxHPq5G1R4gwqzillMxoTo/edit?usp=sharing")

wb1 <- gsheet2tbl("https://docs.google.com/spreadsheets/d/1x3KKDGIwdPQdG3YE5Ekn1iExMrqV76ndJbXAgLe7dsA/edit?usp=sharing")
wb_all <- wb1 %>%
  filter(sample != 0) %>%
  filter(region != "UNEMAT") %>%
  mutate(id = case_when(
    is.na(species) ~ "No",
    TRUE ~ "Yes"
  )) %>%
  mutate(wheat = case_when(
    host == "Triticum aestivum" ~ "Wheat",
    TRUE ~ "Non-wheat"
  )) %>%
  dplyr::select(code, sample, lat, long, host, city, date, year, PstI_specie, species, wheat, DNA_extraction)

set.seed(1000)
wb_all$lat <- round(jitter(wb_all$lat, factor = 1, amount = 0.001), 4)
wb_all$long <- round(jitter(wb_all$long, factor = 1, amount = 0.001), 4)

```



```{r all table, echo=FALSE}
sd <- SharedData$new(wb_all)
```


Dashboard 
============


Column {.sidebar}
-------------------------------------



### Quick filter


```{r}
filter_slider("year", "Select years", sd, ~year)
filter_checkbox("wheat", "Host group", sd, ~wheat, inline = TRUE)
filter_select("host", "Host name", sd, ~host)
filter_checkbox("DNA_extraction", "DNA extracted?", sd, ~DNA_extraction, inline = TRUE)
filter_select("PstI_specie", "Species ID", sd, ~PstI_specie)


```


Column {.tabset}
-------------------------------------


###  Map strains

```{r}
library(RColorBrewer)
library(htmltools)
pal <- colorFactor("Set2", domain = c("Wheat", "Non-wheat"))

leaflet(data = sd, width = "100%") %>%
  setView(-46.8, -20.40, zoom = 6) %>%
  addProviderTiles("Esri.WorldImagery", group = "Aerial") %>%
  addProviderTiles("OpenTopoMap", group = "Terrain") %>%
  addScaleBar("bottomright") %>%
  addProviderTiles(providers$CartoDB.Voyager, group = "Default") %>%
  addLayersControl(
    baseGroups = c("Default", "Aerial", "Terrain"),
    overlayGroups = "Blast pathogen",
    options = layersControlOptions(collapsed = T)
  ) %>%
  addCircleMarkers(
  
    group = "wheat",
    radius = 6,
    fillOpacity = 1,
    weight = 0.5,
    label = paste(wb_all$host, "- Details"),
    fillColor = ~ pal(wheat),

    popup = paste(
      "
Isolate details
",
      "Code:", wb_all$"code", "
",
      "Field sample:", wb_all$"sample", "
",
      "Host:", wb_all$"host", "", "
",
      "Tissue:", wb_all$"tissue", "
",
      "Field sample:", wb_all$"sample", "
",
      "City:", wb_all$"city", "
",
      "Year:", wb_all$"year", "
",
      "DNA extraction:", wb_all$"DNA_extraction", "
",
      "Species:", wb_all$"PstI_specie", "
",
      "OBS:", wb_all$"observation", "", "
"
    )
  ) %>%
  addLegend("bottomleft",
    pal = pal,
    values = ~wheat,
    title = "Host",
    opacity = 1
  ) %>% 
  
  addMeasure(
    position = "bottomleft",
    primaryLengthUnit = "meters",
    primaryAreaUnit = "sqmeters",
    activeColor = "#3D535D",
    completedColor = "#7D4479") %>% 
  addEasyButton(easyButton(
    icon="fa-globe", title="Zoom to Level 3",
    onClick=JS("function(btn, map){ map.setZoom(3); }"))) 
```


###  View grid display


```{r}
datatable(sd,
  extensions = c("Buttons", "ColReorder"),
  escape = TRUE, rownames = FALSE,
  class = "cell-border stripe",
  options = list(
    dom = "Bfrtip", buttons = c("excel", "pdf"), deferRender = TRUE,
    scrollY = 50,
    pageLength = 15,
    scroller = TRUE,
    colReorder = TRUE
  )
)
```




About the project
============


Column {.sidebar}
-------------------------------------



### Participants




Column {.tabset}
-------------------------------------


### About


This is a text

### How to use it